Mining your genes

A successful collaboration between two internationally renowned researchers is using medical science and computer analysis to unlock the mysteries of cancer and other diseases.

Geneticist Professor Rodney Scott and computer scientist Professor Pablo Moscato come from disparate academic backgrounds, but they share a common purpose. The leading researchers are blending their respective knowledge with the aim of making personalised medicine a reality.

Scott and Moscato are co-directors of the University of Newcastle's forward-thinking Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine. As one of only two research sites in Australia that directly link bioinformatics with clinical research practice, it is at the forefront of the emerging field of developing patient-tailored treatments based on genetic analysis.

Both researchers bring considerable expertise to the collaboration. Scott has been working in the field of hereditary diseases for 20 years, and has attracted global recognition for his genetic research, particularly in the areas of breast and bowel cancers.

Moscato began his influential work in computer science in the late 1980s as a member of the Caltech parallel computing group – supercomputing pioneers based at the California Institute of Technology. While there, he developed in collaboration with another researcher a computer optimisation strategy known as a memetic algorithm, now widely used in computation-based applications in many areas of Science and Technology.

What has drawn them together is the need for more efficient ways of processing and appropriately interpret the mass of genetic research data being collected by medical researchers. Working alongside this is the tantalising prospect of being able to use computer profiling technology to customise treatments for individual patients.

"Since I have been working in genetics there has been an explosion of knowledge and huge advances in the technology that can be used to identify risk factors associated with disease," Scott says.

"Technology allows us to acquire a huge amount of data but a bottleneck is created by the analysis, because there is physically so much data to sift through.

"Bioinformatics is providing a mechanism whereby we can reduce the complexity of research data, manage it and interpret it."

Scott and Moscato first collaborated in 2006 when Moscato applied his statistical and computational skills to analysing data associated with the rare genetic disorder xeroderma pigmentosum, a trigger for childhood skin cancer. Scott was impressed with the results and the University, recognising the potential for this valuable interdisciplinary research, approved the investigators' request to set up the centre.

University medical and bioinformatics researchers have since successfully worked together on the interpretation of genetic data relating not only to cancer but a range of conditions including stroke, multiple sclerosis, macular degeneration, Alzheimer's Disease and lung disease.

"When I came to the University in 2002 there was a lot of strength on the clinical side of medical research but not a lot of work underway in bioinformatics," Moscato says.

"I established the Newcastle Bioinformatics Initiative with the support of the university in 2002. On my lead, and with ARC support, Newcastle has been the only NSW node of the ARC Centre of Excellence in Bioinformatics since 2003.

"Now, in some areas, particularly in supercomputing based approaches to interrogate these datasets, we are clearly leading this research field in Australia."

Moscato is pushing the boundaries of molecular interrogation techniques, looking for ways to provide more sophisticated information, including a forensic analysis of data that seeks to explain, rather than dismiss, even minor statistical anomalies. He has developed a method based on Information Theory to track the progession of cancer and Alzheimer's Disease in the brain.

"It is a unifying theory, the Entropic Hallmark," he says.

"A medical researcher can come to us with data that contains a number of variables and our methods are able to highlight the possibilities," he says. "We seek to open new working hypotheses, rather than just give a straightforward reading of the data."

For example, detailed analysis of data over a number of years by his team has led to the identification of what they believe to be the 'genetic signature' of two new subtypes of breast cancer. If validated, the research could lead to new approaches to treatment.

The "final quest", Moscato says, is personalising medicine.

"With cancer, for instance, we are moving away from the approach that there is a silver bullet cure," he says.

"There are thousands of drugs that can be used to treat cancers. That presents a huge number of possible combinations for treatment. Only with sophisticated computer analysis can you screen all of the combinations according to a patient's specific gene characteristics."

Scott picks up the theme: "What we are aiming to achieve is user-friendly programs that can be applied at the clinical level; programs that will efficiently and effectively analyse the data and deliver meaningful information describing a person's risk factors and suggesting optimal treatment."

Professor Rodney Scott and Professor Pablo Moscato research in collaboration with the Hunter Medical Research Institute's (HMRI) Information Based Medicine Program. HMRI is a partnership between the University, Hunter New England Local Health District and the community.

Career Summary

Biography

Inherited forms of cancer have been my main interest for around 20 years. The research I have been involved first focused on the identification of genes associated with with inherited forms of colorectal cancer and breast cancer.

The research area proved to be extremely successful as it really set the scene for our current understanding of the genetic basis of malignancy. Since the identification of genetic susceptibilities my research interests have focused on better defining these inherited entities such that more appropriate intervention strategies can be developed. Initially, much emphasis was placed on recognising genotype/phenotype correlations with disease and as such the research I have undertaken has done much to define such relationships.

More recently, the role of modifier genes in disease penetrance has been a major thematic area and data forthcoming from these studies indicates that there are additional disease susceptibilities that are important in assessing individual risk on a genetic background of high risk. This research is now beginning to be translated to the general population as it represents the first tentative move towards determining cancer risk in the general population. With increasing emphasis on disease prevention it is to be expected that this research will continue to flourish.

My research career took off in Switzerland where I consolidated a centre dedicated to the study of inherited predispositions to cancer. During this period of my research career I was heavily involved in the identification of genetic predispositions to breast cancer and bowel cancer and through my activities supervised 4 PhD students who have since had excellent careers in medical research. The research that I am focused on is consistent with two of Australia's national priorities, healthy aging and a healthy start to life.

Research ExpertiseExpertise in the genetic basis of disease especially in relation to the development of malignancy.

Teaching ExpertiseExpertise in the teaching of medical genetics.

Administrative ExpertiseI have been on numerous State and National committees that are involved in ensuring the delivery of genetic services to the public. I have also served on ethics committees and a variety of other administrative committees.

CollaborationsThe genetics of bowel cancer, Genetic variation and its relationship to disease, The genetics of breast cancer.

Qualifications

Privat Dozent - German equivalent to DSc, University of Basel

Bachelor of Science (Honours), University of Western Australia

PhD, University of Western Australia

Keywords

Cancer Genetics

Colorectal cancer

DNA Repair

DNA repair

Developmental

Gene environment interaction

Genetics

Medical

Molecular

breast cancer

evolution

family studies

genetic epidemiology

homeostasis

human

modifier genes

Languages

German (Fluent)

Fields of Research

Code

Description

Percentage

060499

Genetics not elsewhere classified

40

110399

Clinical Sciences not elsewhere classified

20

111299

Oncology and Carcinogenesis not elsewhere classified

40

Professional Experience

UON Appointment

Title

Organisation / Department

Professor

University of NewcastleSchool of Biomedical Sciences and PharmacyAustralia

Academic appointment

Dates

Title

Organisation / Department

1/06/2005 -

Member gene technology technical advisory committee

Gene Technology Regulator, Federal GovernmentAustralia

1/06/2005 -

Scientific Advisor

Cancer Institute NSW

1/01/2003 -

Chair of the Board of Censors for Molecular Genetics

Human Genetics Society of Australasia (HGSA)Australia

1/01/2002 -

Founding Member

International Hereditary Cancer CenterPoland

1/01/2002 - 1/12/2003

Member of the Working Group on Human Gene Patents

Australian Health Ministers' Advisory Council (AHMAC)Australia

1/04/2000 -

Visiting Professor of Cancer Genetics

Pomeranian Academy of MedicineDepartment of Pathology and GeneticsPoland

1/01/1990 - 1/07/1997

Research Group Leader

University Clinics BaselDepartment of Research and TeachingSwitzerland

Membership

Dates

Title

Organisation / Department

Member - Royal College of Pathologists of Australasia

Royal College of Pathologists of Australasia

Member of the Management Committee

Ramaciotti Centre for Gene Function AnalysisAustralia

Secretary - NSWOG (Familial Cancer) Cancer Institute of NSW

NSWOG (Familial Cancer) Cancer Institute of NSWAustralia

Member of the DNA Working Party

NSW Department of Health

Editor-in-Chief

Hereditary Cancer in Clinical PracticeAustralia

Member - International Network for Cancer Treatment and Research (INCTR)

International Network for Cancer Treatment and Research (INCTR)Australia

We propose here a methodology to uncover modularities in the network of SNPÂ¿SNP interactions most associated with disease. We start by computing all possible Boolean binary SNP i... [more]

We propose here a methodology to uncover modularities in the network of SNPÂ¿SNP interactions most associated with disease. We start by computing all possible Boolean binary SNP interactions across the whole genome. By constructing a weighted graph of the most relevant interactions and via a combinatorial optimization approach, we fnd the most highly interconnected SNPs. We show that the method can be easily extended to fnd SNP/environment interactions. Using a modestly sized GWAS dataset of age-related macular degeneration (AMD), we identify a group of only 19 SNPs, which include those in previously reported regions associated to AMD. We also uncover a larger set of loci pointing to a matrix of key processes and functions that are affected. The proposed integrative methodology extends and overlaps traditional statistical analysis in a natural way. Combinatorial optimization techniques allow us to fnd the kernel of the most central interactions, complementing current methods of GWAS analysis and also enhancing the search for geneÂ¿environment interaction.

It is biologically plausible that a paternal preconception diet low in nutrients related to DNA integrity could affect sperm DNA and subsequently risk of cancer in the offspring. ... [more]

It is biologically plausible that a paternal preconception diet low in nutrients related to DNA integrity could affect sperm DNA and subsequently risk of cancer in the offspring. The aim of this analysis was to investigate whether paternal preconception dietary folate, B6, or B12 intake was associated with the risk of childhood brain tumors (CBT) in an Australian case-control study. Cases <15 years of age were recruited from 10 Australian pediatric oncology centers between 2005 and 2010, and controls from random-digit dialing, frequency-matched to cases on age, sex, and state of residence. Paternal dietary information was obtained by food-frequency questionnaires. Nutrient values were energy adjusted and divided into tertiles for analysis by unconditional logistic regression. In fathers with relevant data (237 cases and 629 controls), no association with dietary folate and B6 and risk of CBT was seen; high B12 intake was associated with an increased risk of CBT (odds ratio highest vs. lowest tertile: 1.74, 95% confidence interval: 1.14, 2.66) without an increasing trend. These results do not support the hypothesis that paternal dietary folate intake influences the risk of CBT. The increased OR observed between dietary B12 intake and risk of CBT is without any certain explanation.

Acute lymphoblastic leukemia (ALL) and childhood brain tumors (CBT) are 2 of the most common forms of childhood cancer, but little is known of their etiology. In 2 nationwide case... [more]

Acute lymphoblastic leukemia (ALL) and childhood brain tumors (CBT) are 2 of the most common forms of childhood cancer, but little is known of their etiology. In 2 nationwide case-control studies we investigated whether breastfeeding, age of food introduction, or early diet are associated with the risk of these cancers. Cases aged 0-14 years were identified from Australian pediatric oncology units between 2003 and 2007 (ALL) and 2005 and 2010 (CBT) and population-based controls through nationwide random-digit dialing. Mothers completed questionnaires giving details of infant feeding up to the age of 2 yr. Data from 322 ALL cases, 679 ALL controls, 299 CBT cases, and 733 CBT controls were analysed using unconditional logistic regression. Breastfeeding was associated with a reduced risk of ALL [odds ratio (OR) = 0.52, 95% confidence interval (CI): 0.32, 0.84), regardless of duration. Introduction of artificial formula within 14 days of birth was positively associated with ALL (OR = 1.57, 95% CI: 1.03, 2.37), as was exclusive formula feeding to 6 mo (OR = 1.81, 95% CI: 1.07, 3.05). No associations were seen between breastfeeding or formula use and risk of CBT. Our results suggest that breastfeeding and delayed introduction of artificial formula may reduce the risk of ALL but not CBT.

Triple-negative breast cancersÂ¿(TNBC) lack expression of oestrogen, progesterone and HER2 receptors. The gene expression profiles of TNBCs are similar to those of breast tumours ... [more]

Triple-negative breast cancersÂ¿(TNBC) lack expression of oestrogen, progesterone and HER2 receptors. The gene expression profiles of TNBCs are similar to those of breast tumours in women with BRCA1 mutations. Reports to date indicate that up to 20Â¿% of TNBC patients harbour germline BRCA mutations; however, the prevalence of BRCA mutations in TNBC patients varies widely between countries and from study to study. We studied 774 women with triple-negative breast cancer, diagnosed on average at age 58.0Â¿years. Samples of genomic DNA were provided by the Australian Breast Cancer Tissue Bank (ABCTB) (439 patients) and by the Department of Genetics and Pathology of the Pomeranian Medical University (335 patients). The entire coding regions and the exonÂ¿intron boundaries of BRCA1 and BRCA2 were amplified and sequenced by next-generation sequencing. We identified a BRCA1 or BRCA2 mutation in 74 of 774 (9.6Â¿%) triple-negative patients. The mutation prevalence was 9.3Â¿% in Australia and was 9.9Â¿% in Poland. In both countries, the mean age of diagnoses of BRCA1 mutation carriers was significantly lower than that of non-carriers, while the age of onset of BRCA2 mutation carriers was similar to that of non-carriers. In the Australian cohort, 59Â¿% of the mutation-positive patients did not have a family history of breast or ovarian cancer, and would not have qualified for genetic testing. The triple-negative phenotype should be added as a criterion to genetic screening guidelines.

Xeroderma pigmentosum (XP) is a rare autosomal recessive disease that is associated with a severe deficiency in nucleotide excision repair. Genetic polymorphisms in XP genes may b... [more]

Xeroderma pigmentosum (XP) is a rare autosomal recessive disease that is associated with a severe deficiency in nucleotide excision repair. Genetic polymorphisms in XP genes may be associated with a change in DNA repair capacity, which could be associated with colorectal cancer development. We assessed the association between 94 single nucleotide polymorphisms (SNPs) within seven XP genes (XPAÂ¿XPG) and the colorectal cancer risk in the Polish population. We genotyped 758 unselected patients with colorectal cancer and 1,841 healthy adults. We found that a significantly decreased risk of colorectal cancer was associated with XPC polymorphism rs2228000_CT genotype (OR 0.59; pÂ¿

Several studies have reported associations between multiple cancer types and single-nucleotide polymorphisms (SNPs) on chromosome 5p15, which harbours TERT and CLPTM1L, but no suc... [more]

Several studies have reported associations between multiple cancer types and single-nucleotide polymorphisms (SNPs) on chromosome 5p15, which harbours TERT and CLPTM1L, but no such association has been reported with endometrial cancer. To evaluate the role of genetic variants at the TERTÂ¿CLPTM1L region in endometrial cancer risk, we carried out comprehensive fine-mapping analyses of genotyped and imputed SNPs using a custom Illumina iSelect array which includes dense SNP coverage of this region. We examined 396 SNPs (113 genotyped, 283 imputed) in 4,401 endometrial cancer cases and 28,758 controls. Single-SNP and forward/backward logistic regression models suggested evidence for three variants independently associated with endometrial cancer risk (PÂ¿=Â¿4.9Â¿ÃÂ¿10-6 to PÂ¿=Â¿7.7Â¿ÃÂ¿10-5). Only one falls into a haplotype previously associated with other cancer types (rs7705526, in TERT intron 1), and this SNP has been shown to alter TERT promoter activity. One of the novel associations (rs13174814) maps to a second region in the TERT promoter and the other (rs62329728) is in the promoter region of CLPTM1L; neither are correlated with previously reported cancer-associated SNPs. Using TCGA RNASeq data, we found significantly increased expression of both TERT and CLPTM1L in endometrial cancer tissue compared with normal tissue (TERTPÂ¿=Â¿1.5Â¿ÃÂ¿10-18, CLPTM1LPÂ¿=Â¿1.5Â¿ÃÂ¿10-19). Our study thus reports a novel endometrial cancer risk locus and expands the spectrum of cancer types associated with genetic variation at 5p15, further highlighting the importance of this region for cancer susceptibility.

Hand grip strength (GS) is a predictor of mortality in older adults and is moderately to highly heritable, but no genetic variants have been consistently identified. We aimed to i... [more]

Hand grip strength (GS) is a predictor of mortality in older adults and is moderately to highly heritable, but no genetic variants have been consistently identified. We aimed to identify single nucleotide polymorphisms (SNPs) associated with GS in middle-aged to older adults using a genome-wide association study (GWAS). GS was measured using handheld dynamometry in community-dwelling men and women aged 55Â¿85 from the Hunter Community Study (HCS, N = 2088) and the Sydney Memory and Ageing Study (Sydney MAS, N = 541). Genotyping was undertaken using Affymetrix microarrays with imputation to HapMap2. Analyses were performed using linear regression. No genome-wide significant results were observed in HCS nor were any of the top signals replicated in Sydney MAS. Gene-based analyses in HCS identified two significant genes (ZNF295, C2CD2), but these results were not replicated in Sydney MAS. One out of eight SNPs previously associated with GS, rs550942, located near the CNTF gene, was significantly associated with GS (p = 0.005) in the HCS cohort only. Study differences may explain the lack of consistent results between the studies, including the smaller sample size of the Sydney MAS cohort. Our modest sample size also had limited power to identify variants of small effect. Our results suggest that similar to various other complex traits, many genetic variants of small effect size may influence GS. Future GWAS using larger samples and consistent measures may prove more fruitful at identifying genetic contributors for GS in middle-aged to older adults.

It is biologically plausible that a paternal preconception diet low in nutrients related to DNA integrity could affect sperm DNA and subsequently risk of cancer in the offspring. ... [more]

It is biologically plausible that a paternal preconception diet low in nutrients related to DNA integrity could affect sperm DNA and subsequently risk of cancer in the offspring. The aim of this analysis was to investigate whether paternal preconception dietary folate, B6, or B12 intake was associated with the risk of childhood brain tumors (CBT) in an Australian case-control study. Cases <15Â¿years of age were recruited from 10 Australian pediatric oncology centers between 2005 and 2010, and controls from random-digit dialing, frequency-matched to cases on age, sex, and state of residence. Paternal dietary information was obtained by food-frequency questionnaires. Nutrient values were energy adjusted and divided into tertiles for analysis by unconditional logistic regression. In fathers with relevant data (237 cases and 629 controls), no association with dietary folate and B6 and risk of CBT was seen; high B12 intake was associated with an increased risk of CBT (odds ratio highest vs. lowest tertile: 1.74, 95% confidence interval: 1.14, 2.66) without an increasing trend. These results do not support the hypothesis that paternal dietary folate intake influences the risk of CBT. The increased OR observed between dietary B12 intake and risk of CBT is without any certain explanation.

The aetiology of childhood brain tumours (CBT) is largely unknown. Damage to germ cells after parental exposure to airborne carcinogens, such as volatile organic compounds and pol... [more]

The aetiology of childhood brain tumours (CBT) is largely unknown. Damage to germ cells after parental exposure to airborne carcinogens, such as volatile organic compounds and polycyclic aromatic hydrocarbons is one plausible pathway. This analysis aimed to investigate whether parental refuelling of vehicles or the use of domestic wood heaters in key time periods relating to the child's birth was associated with an increased risk of CBT. Procedure: Cases <15 years of age were recruited through 10 paediatric oncology centres around Australia; controls were recruited through nationwide random-digit dialling, frequency matched to cases on age, sex and State of residence. Exposure to refuelling and wood heaters was ascertained through questionnaires from both parents. Odds ratios (ORs) and confidence intervals (CIs) were estimated using unconditional logistic regression, adjusting for relevant covariates. Results: Data were available for 306 case and 950 control families. Paternal refuelling =4times/month was associated with an increased risk of CBT (OR 1.59, 95% CI: 1.11, 2.29), and a dose-dependent trend was observed (P=0.004). No association was seen for maternal refuelling. Use of closed, but not open, wood heaters before (OR 1.51, 95% CI: 1.05, 2.15) and after (OR 1.44, 95% CI: 1.03, 2.01) the child's birth was associated with increased risk of CBT, but dose-response relationships were weak or absent. Conclusions: Paternal refuelling of vehicles =4times/month and the use of closed wood heaters before the child's birth may increase the risk of CBT. Replication in larger studies is needed.

Background: Data for multiple common susceptibility alleles for breast cancer may be combined to identify women at different levels of breast cancer risk. Such stratification coul... [more]

Background: Data for multiple common susceptibility alleles for breast cancer may be combined to identify women at different levels of breast cancer risk. Such stratification could guide preventive and screening strategies. However, empirical evidence for genetic risk stratification is lacking. Methods: We investigated the value of using 77 breast cancer-associated single nucleotide polymorphisms (SNPs) for risk stratification, in a study of 33 673 breast cancer cases and 33 381 control women of European origin. We tested all possible pair-wise multiplicative interactions and constructed a 77-SNP polygenic risk score (PRS) for breast cancer overall and by estrogen receptor (ER) status. Absolute risks of breast cancer by PRS were derived from relative risk estimates and UK incidence and mortality rates. Results: There was no strong evidence for departure from a multiplicative model for any SNP pair. Women in the highest 1% of the PRS had a three-fold increased risk of developing breast cancer compared with women in the middle quintile (odds ratio [OR] = 3.36, 95% confidence interval [CI] = 2.95 to 3.83). The ORs for ER-positive and ER-negative disease were 3.73 (95% CI = 3.24 to 4.30) and 2.80 (95% CI = 2.26 to 3.46), respectively. Lifetime risk of breast cancer for women in the lowest and highest quintiles of the PRS were 5.2% and 16.6% for a woman without family history, and 8.6% and 24.4% for a woman with a first-degree family history of breast cancer. Conclusions: The PRS stratifies breast cancer risk in women both with and without a family history of breast cancer. The observed level of risk discrimination could inform targeted screening and prevention strategies. Further discrimination may be achievable through combining the PRS with lifestyle/environmental factors, although these were not considered in this report.

The editors of Hereditary Cancer in Clinical Practice would like to thank all our reviewers who have contributed to the journal in 2014. Without the participation of skilful revie... [more]

The editors of Hereditary Cancer in Clinical Practice would like to thank all our reviewers who have contributed to the journal in 2014. Without the participation of skilful reviewers, no academic journal could succeed, and we are grateful to the committed individuals who have given their time and expertise to the peer review of manuscripts for Hereditary Cancer in Clinical Practice. We look forward to your continued support in 2015.

Infiltration of the tumor microenvironment by nerve fibers is an understudied aspect of breast carcinogenesis. In this study, the presence of nerve fibers was investigated in a co... [more]

Infiltration of the tumor microenvironment by nerve fibers is an understudied aspect of breast carcinogenesis. In this study, the presence of nerve fibers was investigated in a cohort of 369 primary breast cancers (ductal carcinomas in situ, invasive ductal and lobular carcinomas) by immunohistochemistry for the neuronal marker PGP9.5. Isolated nerve fibers (axons) were detected in 28% of invasive ductal carcinomas as compared to only 12% of invasive lobular carcinomas and 8% of ductal carcinomas in situ (p=0.0003). In invasive breast cancers, the presence of nerve fibers was observed in 15% of lymph node negative tumors and 28% of lymph node positive tumors (p=0.0031), indicating a relationship with the metastatic potential. In addition, there was an association between the presence of nerve fibers and the expression of nerve growth factor (NGF) in cancer cells (p=0.0001). Invitro, breast cancer cells were able to induce neurite outgrowth in PC12 cells, and this neurotrophic activity was partially inhibited by anti-NGF blocking antibodies. In conclusion, infiltration by nerve fibers is a feature of the tumor microenvironment that is associated with aggressiveness and involves NGF production by cancer cells. The potential participation of nerve fibers in breast cancer progression needs to be further considered.

Genome-wide association studies have identified SNPs near ZNF365 at 10q21.2 that are associated with both breast cancer risk and mammographic density. To identify the most likely ... [more]

Genome-wide association studies have identified SNPs near ZNF365 at 10q21.2 that are associated with both breast cancer risk and mammographic density. To identify the most likely causal SNPs, we fine mapped the association signal by genotyping 428 SNPs across the region in 89,050 European and 12,893 Asian case and control subjects from the Breast Cancer Association Consortium. We identified four independent sets of correlated, highly trait-associated variants (iCHAVs), three of which were located within ZNF365. The most strongly risk-associated SNP, rs10995201 in iCHAV1, showed clear evidence of association with both estrogen receptor (ER)-positive (OR = 0.85 [0.82-0.88]) and ER-negative (OR = 0.87 [0.82-0.91]) disease, and was also the SNP most strongly associated with percent mammographic density. iCHAV2 (lead SNP, chr10: 64,258,684:D) and iCHAV3 (lead SNP, rs7922449) were also associated with ER-positive (OR = 0.93 [0.91-0.95] and OR = 1.06 [1.03-1.09]) and ER-negative (OR = 0.95 [0.91-0.98] and OR = 1.08 [1.04-1.13]) disease. There was weaker evidence for iCHAV4, located 5' of ADO, associated only with ER-positive breast cancer (OR = 0.93 [0.90-0.96]). We found 12, 17, 18, and 2 candidate causal SNPs for breast cancer in iCHAVs 1-4, respectively. Chromosome conformation capture analysis showed that iCHAV2 interacts with the ZNF365 and NRBF2 (more than 600 kb away) promoters in normal and cancerous breast epithelial cells. Luciferase assays did not identify SNPs that affect transactivation of ZNF365, but identified a protective haplotype in iCHAV2, associated with silencing of the NRBF2 promoter, implicating this gene in the etiology of breast cancer.

Children with the recessive genetic disorder Xeroderma Pigmentosum (XP) have extreme sensitivity to UV-light, a 10,000-fold increase in skin cancers from age 2 and rarely live bey... [more]

Children with the recessive genetic disorder Xeroderma Pigmentosum (XP) have extreme sensitivity to UV-light, a 10,000-fold increase in skin cancers from age 2 and rarely live beyond 30 years. There are seven genetic subgroups of XP, which are all resultant of pathogenic mutations in genes in the nucleotide excision repair (NER) pathway and a XP variant resultant of a mutation in translesion synthesis, POLH. The clinical symptoms and severity of the disease is varied across the subgroups, which does not correlate with the functional position of the affected protein in the NER pathway. The aim of this study was to further understand the biology of XP subgroups, particularly those that manifest with neurological symptoms. Whole genome gene expression profiling of fibroblasts from each XP complementation group was assessed before and after UV-light exposure. The biological pathways with altered gene expression after UV-light exposure were distinct for each subtype and contained oncogenic related functions such as perturbation of cell cycle, apoptosis, proliferation and differentiation. Patients from the subgroups XP-B and XP-F were the only subgroups to have transcripts associated with neuronal activity altered after UV-light exposure. This study will assist in furthering our understanding of the different subtypes of XP which will lead to better diagnosis, treatment and management of the disease.

In 2011, Watson and Barnes proposed a schema for classifying biobanks into 3 groups (mono-, oligo-, and poly-user), primarily based upon biospecimen access policies. We used resul... [more]

In 2011, Watson and Barnes proposed a schema for classifying biobanks into 3 groups (mono-, oligo-, and poly-user), primarily based upon biospecimen access policies. We used results from a recent comprehensive survey of cancer biobanks in New South Wales, Australia to assess the applicability of this biobank classification schema in an Australian setting. Cancer biobanks were identified using publically available data, and by consulting with research managers. A comprehensive survey was developed and administered through a face-to-face setting. Data were analyzed using Microsoft ExcelÂ¿ 2010 and IBM SPSS StatisticsÂ¿ version 21.0. The cancer biobank cohort (n=23) represented 5 mono-user biobanks, 7 oligo-user biobanks, and 11 poly-user biobanks, and was analyzed as two groups (mono-/oligo- versus poly-user biobanks). Poly-user biobanks employed significantly more full-time equivalent staff, and were significantly more likely to have a website, share staff between biobanks, access governance support, utilize quality control measures, be aware of biobanking best practice documents, and offer staff training. Mono-/oligo-user biobanks were significantly more likely to seek advice from other biobanks. Our results further delineate a biobank classification system that is primarily based on access policy, and demonstrate its relevance in an Australian setting.

We propose here a methodology to uncover modularities in the network of SNP-SNP interactions most associated with disease. We start by computing all possible Boolean binary SNP in... [more]

We propose here a methodology to uncover modularities in the network of SNP-SNP interactions most associated with disease. We start by computing all possible Boolean binary SNP interactions across the whole genome. By constructing a weighted graph of the most relevant interactions and via a combinatorial optimization approach, we find the most highly interconnected SNPs. We show that the method can be easily extended to find SNP/environment interactions. Using a modestly sized GWAS dataset of age-related macular degeneration (AMD), we identify a group of only 19 SNPs, which include those in previously reported regions associated to AMD. We also uncover a larger set of loci pointing to a matrix of key processes and functions that are affected. The proposed integrative methodology extends and overlaps traditional statistical analysis in a natural way. Combinatorial optimization techniques allow us to find the kernel of the most central interactions, complementing current methods of GWAS analysis and also enhancing the search for gene-environment interaction.

Human genetic and animal studies have implicated the costimulatory molecule CD40 in the development of multiple sclerosis (MS). We investigated the cell specific gene and protein ... [more]

Human genetic and animal studies have implicated the costimulatory molecule CD40 in the development of multiple sclerosis (MS). We investigated the cell specific gene and protein expression variation controlled by the CD40 genetic variant(s) associated with MS, i.e. the T-allele at rs1883832. Previously we had shown that the risk allele is expressed at a lower level in whole blood, especially in people with MS. Here, we have defined the immune cell subsets responsible for genotype and disease effects on CD40 expression at the mRNA and protein level. In cell subsets in which CD40 is most highly expressed, B lymphocytes and dendritic cells, the MS-associated risk variant is associated with reduced CD40 cell-surface protein expression. In monocytes and dendritic cells, the risk allele additionally reduces the ratio of expression of full-length versus truncated CD40 mRNA, the latter encoding secreted CD40. We additionally show that MS patients, regardless of genotype, express significantly lower levels of CD40 cell-surface protein compared to unaffected controls in B lymphocytes. Thus, both genotype-dependent and independent down-regulation of cell-surface CD40 is a feature of MS. Lower expression of a co-stimulator of T cell activation, CD40, is therefore associated with increased MS risk despite the same CD40 variant being associated with reduced risk of other inflammatory autoimmune diseases. Our results highlight the complexity and likely individuality of autoimmune pathogenesis, and could be consistent with antiviral and/or immunoregulatory functions of CD40 playing an important role in protection from MS.

The risk factors for sudden infant death syndrome (SIDS) parallel those associated with susceptibility to or severity of infectious diseases. There is no evidence that a single in... [more]

The risk factors for sudden infant death syndrome (SIDS) parallel those associated with susceptibility to or severity of infectious diseases. There is no evidence that a single infectious agent is associated with SIDS; the common thread appears to be induction of inflammatory responses to infections. In this review, interactions between genetic and environmental risk factors for SIDS are assessed in relation to the hypothesis that many infant deaths result from dysregulation of inflammatory responses to "minor" infections. Risk factors are assessed in relation to three important stages of infection: (1) bacterial colonization (frequency or density); (2) induction of temperature-dependent toxins; (3) induction or control of inflammatory responses. In this article, we review the interactions among risk factors for SIDS for their effects on induction or control of inflammatory responses. The risk factors studied are genetic factors (sex, cytokine gene polymorphisms among ethnic groups at high or low risk of SIDS); developmental stage (changes in cortisol and testosterone levels associated with 2- to 4-month age range); environmental factors (virus infection, exposure to cigarette smoke). These interactions help to explain differences in the incidences of SIDS observed between ethnic groups prior to public health campaigns to reduce these infant deaths.

Glaucoma is characterized by irreversible optic nerve degeneration and is the most frequent cause of irreversible blindness worldwide. Here, the International Glaucoma Genetics Co... [more]

Glaucoma is characterized by irreversible optic nerve degeneration and is the most frequent cause of irreversible blindness worldwide. Here, the International Glaucoma Genetics Consortium conducts a meta-analysis of genome-wide association studies of vertical cup-disc ratio (VCDR), an important disease-related optic nerve parameter. In 21,094 individuals of European ancestry and 6,784 individuals of Asian ancestry, we identify 10 new loci associated with variation in VCDR. In a separate risk-score analysis of five case-control studies, Caucasians in the highest quintile have a 2.5-fold increased risk of primary open-angle glaucoma as compared with those in the lowest quintile. This study has more than doubled the known loci associated with optic disc cupping and will allow greater understanding of mechanisms involved in this common blinding condition.

Endometrial cancer is the most common invasive gynaecological cancer in women, and relatively little is known about inherited risk factors for this disease. This is the first geno... [more]

Endometrial cancer is the most common invasive gynaecological cancer in women, and relatively little is known about inherited risk factors for this disease. This is the first genome-wide study to explore the role of common and rare germline copy number variants (CNVs) in predisposition to endometrial cancer. CNVs were called from germline DNA of 1,209 endometrioid endometrial cancer cases and 528 cancer-unaffected female controls. Overall CNV load of deletions or DNA gains did not differ significantly between cases and controls (P > 0.05), but cases presented with an excess of rare germline deletions overlapping likely functional genomic regions including genes (P = 8 Ã 10-10), CpG islands (P = 1 Ã 10-7) and sno/miRNAs regions (P = 3 Ã 10-9). On average, at least one additional gene and two additional CpG islands were disrupted by rare deletions in cases compared to controls. The most pronounced difference was that over 30 sno/miRNAs were disrupted by rare deletions in cases for every single disruption event in controls. A total of 13 DNA repair genes were disrupted by rare deletions in 19/1,209 cases (1.6 %) compared to one gene in 1/528 controls (0.2 %; P = 0.007), and this increased DNA repair gene loss in cases persisted after excluding five individuals carrying CNVs disrupting mismatch repair genes MLH1, MSH2 and MSH6 (P = 0.03). There were 34 miRNA regions deleted in at least one case but not in controls, the most frequent of which encompassed hsa-mir-661 and hsa-mir-203. Our study implicates rare germline deletions of functional and regulatory regions as possible mechanisms conferring endometrial cancer risk, and has identified specific regulatory elements as candidates for further investigation.

Several studies have reported associations between multiple cancer types and single-nucleotide polymorphisms (SNPs) on chromosome 5p15, which harbours TERT and CLPTM1L, but no suc... [more]

Several studies have reported associations between multiple cancer types and single-nucleotide polymorphisms (SNPs) on chromosome 5p15, which harbours TERT and CLPTM1L, but no such association has been reported with endometrial cancer. To evaluate the role of genetic variants at the TERTÂ¿CLPTM1L region in endometrial cancer risk, we carried out comprehensive fine-mapping analyses of genotyped and imputed SNPs using a custom Illumina iSelect array which includes dense SNP coverage of this region. We examined 396 SNPs (113 genotyped, 283 imputed) in 4,401 endometrial cancer cases and 28,758 controls. Single-SNP and forward/backward logistic regression models suggested evidence for three variants independently associated with endometrial cancer risk (P = 4.9 Ã 10-6 to P = 7.7 Ã 10-5). Only one falls into a haplotype previously associated with other cancer types (rs7705526, in TERT intron 1), and this SNP has been shown to alter TERT promoter activity. One of the novel associations (rs13174814) maps to a second region in the TERT promoter and the other (rs62329728) is in the promoter region of CLPTM1L; neither are correlated with previously reported cancer-associated SNPs. Using TCGA RNASeq data, we found significantly increased expression of both TERT and CLPTM1L in endometrial cancer tissue compared with normal tissue (TERTP = 1.5 Ã 10-18, CLPTM1LP = 1.5 Ã 10-19). Our study thus reports a novel endometrial cancer risk locus and expands the spectrum of cancer types associated with genetic variation at 5p15, further highlighting the importance of this region for cancer susceptibility.

The genetic basis of prostate cancer (PC) is complex and appears to involve multiple susceptibility genes. A number of studies have evaluated a possible correlation between severa... [more]

The genetic basis of prostate cancer (PC) is complex and appears to involve multiple susceptibility genes. A number of studies have evaluated a possible correlation between several NER gene polymorphisms and PC risk, but most of them evaluated only single SNPs among XP genes and the results remain inconsistent. Out of 94 SNPs located in seven XP genes (XPA-. XPG) a total of 15 SNPs were assayed in 720 unselected patients with PC and compared to 1121 healthy adults. An increased risk of disease was associated with the XPD SNP, rs1799793 (Asp312Asn) AG genotype (OR. = 2.60; p.

There are a growing number of large cohorts of older persons with genome-wide genotyping data available, but APOE is not included in any of the common microarray platforms. We com... [more]

There are a growing number of large cohorts of older persons with genome-wide genotyping data available, but APOE is not included in any of the common microarray platforms. We compared directly measured APOE genotypes with those imputed using microarray data and the '1000 Genomes' dataset in a sample of 320 Caucasians. We find 90% agreement for e2/e3/e4 genotypes and 93% agreement for predicting e4 status, yielding kappa values of 0.81 and 0.84, respectively. More stringent thresholds around allele number estimates can increase this agreement to 90-97% and kappas of 0.90-0.93.

Attia JR, Ioannidis JPA, Thakkinstian A, McEvoy MA, Scott R, Minelli C, et al., 'How to use an article about genetic association C: What are the results and will they help me in caring for my patients?', JAMA: Journal of the American Medical Association, 301 304-308 (2009) [C1]

Scott R, 'Response to 'Variability in the clinical phenotype among families with HNPCC': The potential importance of the location of the mutation in the gene by Dr. Prathap Bandipalliant', International Journal of Cancer, 120 2278 (2007) [C3]

Recent advances in our understanding of the genetic basis of several inherited predispositions to cancer have raised the possibility that there may be differences in prognosis bet... [more]

Recent advances in our understanding of the genetic basis of several inherited predispositions to cancer have raised the possibility that there may be differences in prognosis between patients harbouring genetic susceptibilities to cancer and persons presenting with sporadic disease. The two best studied models of inherited susceptibilities to cancer will be considered, those of colorectal cancer and familial breast cancer. Familial colorectal cancer can be subdivided into essentially two groups: familial adenomatous polyposis and hereditary non-polyposis colorectal cancer. Familial breast cancer can be subdivided into three groups: those that can be accounted for by mutations in the breast cancer susceptibility gene BRCA 1, families harbouring mutations in BRCA 2 and families where neither BRCA 1 nor BRCA 2 appear to be involved. In this chapter several aspects of these inherited cancer predispositions will be discussed and compared with their equivalent sporadic disease counterparts.

Several BRCA2 mutations are found to occur in geographically diverse breast and ovarian cancer families. To investigate both mutation origin and mutation-specific phenotypes due t... [more]

Several BRCA2 mutations are found to occur in geographically diverse breast and ovarian cancer families. To investigate both mutation origin and mutation-specific phenotypes due to BRCA2, we constructed a haplotype of 10 polymorphic short tandem-repeat (STR) markers flanking the BRCA2 locus, in a set of 111 breast or breast/ovarian cancer families selected for having one of nine recurrent BRCA2 mutations. Six of the individual mutations are estimated to have arisen 400-2,000 years ago. In particular, the 6174delT mutation, found in ~1% of individuals of Ashkenazi Jewish ancestry, was estimated to have arisen 29 generations ago (1-LOD support interval 22-38). This is substantially more recent than the estimated age of the BRCA1 185delAG mutation (46 generations), derived from our analogous study of BRCA1 mutations. In general, there was no evidence of multiple origins of identical BRCA2 muta- tions. Our study data were consistent with the previous report of a higher incidence of ovarian cancer in families with mutations in a 3.3-kb region of exon 11 (the ovarian cancer cluster region [OCCR]) (P = .10); but that higher incidence was not statistically significant. There was significant evidence that age at diagnosis of breast cancer varied by mutation (P < .001), although only 8% of the variance in age at diagnosis could be explained by the specific mutation, and there was no evidence of family-specific effects. When the age at diagnosis of the breast cancer cases was examined by OCCR, cases associated with mutations in the OCCR had a significantly older mean age at diagnosis than was seen in those outside this region (48 years vs. 42 years; P = .0005).

Eighty-six women fulfilling specific selection criteria were studied for germline mutations in two breast cancer susceptibility genes, BRCA1 and BRCA2, using the protein truncation test (PTT). Nine germline mutations were identified, six in BRCA1 and three in BRCA2. Of the six BRCA1 mutations, three have previously been described and three are new, and for BRCA2, one is a new mutation and the other two appear to occur at a site that has been described several times. Four kindreds were breast cancer families, one a breast/ovarian cancer family, and the sixth an ovarian cancer family. The three kindreds with BRCA2 mutations were classified as one breast/ovarian cancer family, one breast cancer family, and one family which harboured one early onset breast cancer patient and two melanoma patients. The mutations in BRCA1 were either insertions, deletions, or transitions which all resulted in a premature stop codon. Mutations in BRCA2 were all frameshift mutations as a result of either 2 or 4 bp deletions. Two BRCA2 mutations were identical, suggesting a Swiss founder effect which was confirmed by haplotype sharing. The 10% mutation detection rate is compatible with the relaxed criteria used for patient selection. Considering the relative ease with which coding sequences can be screened by PTT, this assay is useful as a first screen for BRCA1 and BRCA2 mutations.

Modifier Genes in Lynch Syndrome: Functional Genomics and its Consequence on Disease ExpressionHealth, Faculty of Health and MedicineSole Supervisor

2011

Microarray Studies of Genome-Wide Changes in Brain and Heart Gene Expression in Mouse Models of Iron OverloadHealth, Faculty of Health and MedicineCo-Supervisor

2011

Susceptibility to and Severity of Inflammatory-related Diseases in Indigenous Australians; An In Vitro Investigation of Associated Environmental and Genetic Risk FactorsMicrobiology, Faculty of Health and MedicinePrincipal Supervisor

A HMRI genetics laboratory at Newcastle's John Hunter Hospital has become the first in Australia, and one of the few in the world, to receive accreditation for a new diagnostic system that revolutionises 'NextGen' DNA sequencing for breast and ovarian cancer.